Lep-Anchor Code

#awk [-vprefix=CHR -vlg=1 -vgapLength=100] -f makeagp.awk chr1.la
BEGIN{
	map["+"]="+"
	map["++"]="+"
	map["+++"]="+"
	map["-"]="-"
	map["--"]="-"
	map["---"]="-"
	map[""]="+"
	map["?"]="+"
	if (lg == "")
		lg = 1
	if (prefix == "")
		prefix = "CHR"
	suffix = 1
	if (gapLength == "")
		gapLength = 100
}

(/^[^#]/ && /^[^$]/ && $3-$2>=0){
	if (n != "") {
		if ($4=="?" || (($4 == "+" || $4 == "-") && (prevO != "+" && prevO != "-")) || (($4 == "++" || $4 == "--") && (prevO != "++" && prevO != "--")) || (($4 == "+++" || $4 == "---") && (prevO != "+++" && prevO != "---"))) {
			++suffix
			pos = 0
			n = ""
		} else if (gapLength > 0){
			print prefix lg "." suffix "\t" pos + 1 "\t" pos + gapLength "\t" ++n "\tU\t" gapLength "\tcontig\tno\tna"
			pos += gapLength
		}
	}
	print prefix lg "." suffix "\t" pos + 1 "\t" pos + ($3-$2+1)  "\t" ++n "\tW\t" $1 "\t" $2 "\t" $3 "\t" map[$4]
	pos += ($3-$2+1)
	prevO = $4
}